Since the problem is not caused by JoomSEF, I can only offer you our paid support services to check your website's configuration and try to find what's causing the problem.
If you're interested, please purchase 1 hour of our support time at
www.artio.net/e-shop/support-services/joomla-related-support-1h and contact me at
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with your order number and access credentials to your website's administration area and FTP and we'll check what's causing the template problems. However since I don't know yet what's the cause, I can't promise we'll be able to fix it in the one hour time and depending on the cause there may be more time required to fix it.